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Add new rules visualizing CARLISLE results #132

Merged
merged 23 commits into from
Jun 12, 2024
Merged

Add new rules visualizing CARLISLE results #132

merged 23 commits into from
Jun 12, 2024

Commits on May 15, 2024

  1. Removed temp output

    epehrsson committed May 15, 2024
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Commits on May 21, 2024

  1. Created rules cov_correlation, count_peaks

    epehrsson committed May 21, 2024
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  2. Added rule homer_enrich to plot enrichment over features

    epehrsson committed May 21, 2024
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Commits on May 22, 2024

  1. Added rule combine_homer, requiring change to MACS2 peak xls name

    epehrsson committed May 22, 2024
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  2. Added rule combine_homer, requiring change to MACS2 peak xls name

    epehrsson committed May 22, 2024
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  3. Changed script names, updated changelog

    epehrsson committed May 22, 2024
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Commits on May 23, 2024

  1. Fixed bug assigning colors to many samples

    epehrsson committed May 23, 2024
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  2. Resolve merge commits

    epehrsson committed May 23, 2024
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  3. Reverted temp output

    epehrsson committed May 23, 2024
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Commits on May 29, 2024

  1. Merge branch 'main' into corr-docker

    @kelly-sovacool
    kelly-sovacool committed May 29, 2024
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  2. refactor: use docker container for new R rules

    @kelly-sovacool
    kelly-sovacool committed May 29, 2024
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  3. fix: ComplexHeatmap is on bioc, not cran

    @kelly-sovacool
    kelly-sovacool committed May 29, 2024
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  4. ci: use mamba env create

    @kelly-sovacool
    kelly-sovacool committed May 29, 2024
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  5. chore: Merge branch 'main' into corr-docker

    @kelly-sovacool
    kelly-sovacool committed May 29, 2024
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Commits on May 30, 2024

  1. Merge pull request #1 from CCBR/corr-docker 

    Update docker for new viz rules
    @epehrsson
    epehrsson authored May 30, 2024
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Commits on May 31, 2024

  1. Update workflow/rules/annotations.smk 

    Update input files for homer_enrich to include non-MACS2 treatment-control lists

Co-authored-by: Kelly Sovacool <[email protected]>
    @epehrsson @kelly-sovacool
    epehrsson and kelly-sovacool authored May 31, 2024
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  2. chore: Merge branch 'main' into corr-merge

    @kelly-sovacool
    kelly-sovacool committed May 31, 2024
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  3. Merge pull request #2 from CCBR/corr-merge 

    fix merge conflicts in CCBR/main
    @epehrsson
    epehrsson authored May 31, 2024
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  4. fix: ignore "#" comment lines in peaks files 

    also refactor combine_homer Rscript to use tidyverse
    @kelly-sovacool
    kelly-sovacool committed May 31, 2024
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Commits on Jun 7, 2024

  1. fix: only load needed packages 

    Patrick had a transient error with library(tidyverse) where it failed to load stringr
    @kelly-sovacool
    kelly-sovacool committed Jun 7, 2024
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Commits on Jun 10, 2024

  1. feat: write both tsv & excel format

    @kelly-sovacool
    kelly-sovacool committed Jun 10, 2024
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Commits on Jun 11, 2024

  1. Merge pull request #3 from CCBR/fix-combine-homer 

    fix: ignore "#" comment lines in peaks files
    @epehrsson
    epehrsson authored Jun 11, 2024
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Commits on Jun 12, 2024

  1. Added Excel back to combine_homer output

    epehrsson committed Jun 12, 2024
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